Select local alignment or end-to-end alignment for Bowtie2 to filter rRNA

Question

[Mort]

Hello, I have been working on the metatranscriptomics (2x150 bp), and I want to use Bowtie2 to align the adapter-free and high-quality sequences to the Silva rRNA database, to remove the mapped rRNA reads.

Because the reference sequences is longer than those in metatranscriptomics, I think the local alignment should be better.

Could you please give me some advices?

Thanks in advance!

Mort

[GenoMax]

Consider using a tool like SortMeRNA (LINK).